WHAT IF Check report

This file was created 2012-01-19 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb1xwn.ent

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A; Model number 1

Note: Ramachandran plot

Chain identifier: A; Model number 2

Note: Ramachandran plot

Chain identifier: A; Model number 3

Note: Ramachandran plot

Chain identifier: A; Model number 4

Note: Ramachandran plot

Chain identifier: A; Model number 5

Note: Ramachandran plot

Chain identifier: A; Model number 6

Note: Ramachandran plot

Chain identifier: A; Model number 7

Note: Ramachandran plot

Chain identifier: A; Model number 8

Note: Ramachandran plot

Chain identifier: A; Model number 9

Note: Ramachandran plot

Chain identifier: A; Model number 10

Note: Ramachandran plot

Chain identifier: A; Model number 11

Note: Ramachandran plot

Chain identifier: A; Model number 12

Note: Ramachandran plot

Chain identifier: A; Model number 13

Note: Ramachandran plot

Chain identifier: A; Model number 14

Note: Ramachandran plot

Chain identifier: A; Model number 15

Note: Ramachandran plot

Chain identifier: A; Model number 16

Note: Ramachandran plot

Chain identifier: A; Model number 17

Note: Ramachandran plot

Chain identifier: A; Model number 18

Note: Ramachandran plot

Chain identifier: A; Model number 19

Note: Ramachandran plot

Chain identifier: A; Model number 20

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 MET   (   1-)  A    Zero
   2 ALA   (   2-)  A    Zero
   3 ALA   (   3-)  A    Zero
   4 ILE   (   4-)  A    Zero
   5 PRO   (   5-)  A    Zero
   6 PRO   (   6-)  A    Zero
   7 ASP   (   7-)  A    Zero
   8 SER   (   8-)  A    Zero
   9 TRP   (   9-)  A    Zero
  10 GLN   (  10-)  A    Zero
  11 PRO   (  11-)  A    Zero
  12 PRO   (  12-)  A    Zero
  13 ASN   (  13-)  A    Zero
  14 VAL   (  14-)  A    Zero
  15 TYR   (  15-)  A    Zero
  16 LEU   (  16-)  A    Zero
  17 GLU   (  17-)  A    Zero
  18 THR   (  18-)  A    Zero
  19 SER   (  19-)  A    Zero
  20 MET   (  20-)  A    Zero
  21 GLY   (  21-)  A    Zero
  22 ILE   (  22-)  A    Zero
  23 ILE   (  23-)  A    Zero
  24 VAL   (  24-)  A    Zero
  25 LEU   (  25-)  A    Zero
And so on for a total of 3320 lines.

Geometric checks

Note: Per-model averages for bond-length check

The table below gives the per-model bond-length RMS Z-scores.

Model 1 : 0.270
Model 2 : 0.262
Model 3 : 0.279
Model 4 : 0.268
Model 5 : 0.265
Model 6 : 0.276
Model 7 : 0.269
Model 8 : 0.269
Model 9 : 0.279
Model 10 : 0.274
Model 11 : 0.279
Model 12 : 0.274
Model 13 : 0.284
Model 14 : 0.289
Model 15 : 0.288
Model 16 : 0.291
Model 17 : 0.267
Model 18 : 0.269
Model 19 : 0.280
Model 20 : 0.282

Warning: Directionality in bond lengths

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation.

Since this is not an XRAY structure this effect is hard to explain.

Note: Per-model averages for bond-angle check

The table below gives the per-model bond-angle RMS Z-scores.

Model 1 : 0.388
Model 2 : 0.386
Model 3 : 0.394
Model 4 : 0.385
Model 5 : 0.390
Model 6 : 0.387
Model 7 : 0.388
Model 8 : 0.383
Model 9 : 0.399
Model 10 : 0.394
Model 11 : 0.392
Model 12 : 0.395
Model 13 : 0.399
Model 14 : 0.393
Model 15 : 0.398
Model 16 : 0.396
Model 17 : 0.394
Model 18 : 0.390
Model 19 : 0.395
Model 20 : 0.389

Note: Per-model averages for chirality check

The table below gives the per-model improper dihedral RMS Z-scores.

Model 1 : 0.286
Model 2 : 0.288
Model 3 : 0.285
Model 4 : 0.292
Model 5 : 0.284
Model 6 : 0.277
Model 7 : 0.287
Model 8 : 0.296
Model 9 : 0.290
Model 10 : 0.283
Model 11 : 0.285
Model 12 : 0.287
Model 13 : 0.283
Model 14 : 0.276
Model 15 : 0.281
Model 16 : 0.290
Model 17 : 0.285
Model 18 : 0.285
Model 19 : 0.292
Model 20 : 0.282

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -4.967

Note: Per-model averages for Ramachandran check

The table below gives the per-model Ramachandran Z-scores.

Model 1 : -5.362
Model 2 : -5.661
Model 3 : -4.075
Model 4 : -4.330
Model 5 : -5.367
Model 6 : -4.359
Model 7 : -5.203
Model 8 : -4.821
Model 9 : -4.549
Model 10 : -4.637
Model 11 : -5.242
Model 12 : -4.685
Model 13 : -5.483
Model 14 : -4.942
Model 15 : -4.409
Model 16 : -4.965
Model 17 : -5.267
Model 18 : -5.595
Model 19 : -5.210
Model 20 : -5.179

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

2218 PHE   (  60-)  A 1   -3.8
2558 THR   (  68-)  A 1   -3.6
2060 THR   (  68-)  A 1   -3.6
1562 THR   (  68-)  A 1   -3.6
2550 PHE   (  60-)  A 1   -3.6
3080 PHE   (  92-)  A 1   -3.4
2882 PHE   (  60-)  A 1   -3.4
2724 THR   (  68-)  A 1   -3.4
3056 THR   (  68-)  A 1   -3.3
 451 THR   ( 119-)  A    -3.3
1894 THR   (  68-)  A 1   -3.3
 273 THR   ( 107-)  A    -3.3
1720 PHE   (  60-)  A 1   -3.3
 400 THR   (  68-)  A    -3.3
1249 HIS   (  87-)  A    -3.2
 234 THR   (  68-)  A    -3.2
1752 PHE   (  92-)  A 1   -3.2
1747 HIS   (  87-)  A 1   -3.2
 253 HIS   (  87-)  A    -3.2
1586 PHE   (  92-)  A 1   -3.2
1913 HIS   (  87-)  A 1   -3.1
 937 THR   ( 107-)  A    -3.1
 724 PHE   (  60-)  A    -3.1
  70 THR   (  70-)  A    -3.0
2111 THR   ( 119-)  A 1   -3.0
And so on for a total of 500 lines.

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

   2 ALA   (   2-)  A  Poor phi/psi
  10 GLN   (  10-)  A  Poor phi/psi
  59 ASP   (  59-)  A  Poor phi/psi
  60 PHE   (  60-)  A  Poor phi/psi
  67 PRO   (  67-)  A  Poor phi/psi
  68 THR   (  68-)  A  Poor phi/psi
 106 ASP   ( 106-)  A  Poor phi/psi
 129 PHE   ( 129-)  A  Poor phi/psi
 135 GLY   ( 135-)  A  Poor phi/psi
 169 ALA   (   3-)  A  Poor phi/psi
 173 ASP   (   7-)  A  Poor phi/psi
 212 GLY   (  46-)  A  Poor phi/psi
 219 PHE   (  53-)  A  Poor phi/psi
 225 ASP   (  59-)  A  Poor phi/psi
 226 PHE   (  60-)  A  Poor phi/psi
 234 THR   (  68-)  A  Poor phi/psi
 247 GLN   (  81-)  A  Poor phi/psi
 272 ASP   ( 106-)  A  Poor phi/psi
 301 GLY   ( 135-)  A  Poor phi/psi
 317 ASP   ( 151-)  A  Poor phi/psi
 378 GLY   (  46-)  A  Poor phi/psi
 382 GLY   (  50-)  A  Poor phi/psi
 391 ASP   (  59-)  A  Poor phi/psi
 392 PHE   (  60-)  A  Poor phi/psi
 400 THR   (  68-)  A  Poor phi/psi
And so on for a total of 215 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -7.381

Note: Per-model averages for chi-1/chi-2 angle check

The table below gives the per-model chi-1/chi-2 correlation Z-scores.

Model 1 : -7.698
Model 2 : -7.321
Model 3 : -7.268
Model 4 : -7.615
Model 5 : -7.282
Model 6 : -7.196
Model 7 : -7.348
Model 8 : -7.202
Model 9 : -7.904
Model 10 : -7.388
Model 11 : -7.538
Model 12 : -7.530
Model 13 : -7.449
Model 14 : -7.723
Model 15 : -7.396
Model 16 : -7.403
Model 17 : -6.979
Model 18 : -7.051
Model 19 : -7.366
Model 20 : -6.971

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   6 PRO   (   6-)  A      0
   9 TRP   (   9-)  A      0
  10 GLN   (  10-)  A      0
  11 PRO   (  11-)  A      0
  20 MET   (  20-)  A      0
  29 TRP   (  29-)  A      0
  31 HIS   (  31-)  A      0
  33 PRO   (  33-)  A      0
  47 TYR   (  47-)  A      0
  49 ASN   (  49-)  A      0
  55 ARG   (  55-)  A      0
  58 LYS   (  58-)  A      0
  60 PHE   (  60-)  A      0
  61 MET   (  61-)  A      0
  66 ASP   (  66-)  A      0
  67 PRO   (  67-)  A      0
  68 THR   (  68-)  A      0
  70 THR   (  70-)  A      0
  72 ARG   (  72-)  A      0
  78 TYR   (  78-)  A      0
  80 LYS   (  80-)  A      0
  81 GLN   (  81-)  A      0
  86 LEU   (  86-)  A      0
  88 PRO   (  88-)  A      0
  90 LEU   (  90-)  A      0
And so on for a total of 1803 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 0.428

Note: Per-model averages for omega angle check

The table below gives the per-model omega angle standard deviations.

Model 1 : 0.364
Model 2 : 0.350
Model 3 : 0.381
Model 4 : 0.362
Model 5 : 0.351
Model 6 : 0.345
Model 7 : 0.396
Model 8 : 0.395
Model 9 : 0.359
Model 10 : 0.369
Model 11 : 0.374
Model 12 : 0.385
Model 13 : 0.386
Model 14 : 0.429
Model 15 : 0.330
Model 16 : 0.417
Model 17 : 0.406
Model 18 : 0.412
Model 19 : 0.339
Model 20 : 0.311

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

2931 GLY   ( 109-)  A 1  2.39   22
3097 GLY   ( 109-)  A 1  2.39   17
1271 GLY   ( 109-)  A   2.38   23
2765 GLY   ( 109-)  A 1  2.28   22
1935 GLY   ( 109-)  A 1  2.18   18
1437 GLY   ( 109-)  A   2.11   15
 275 GLY   ( 109-)  A   2.11   11
1105 GLY   ( 109-)  A   2.10   18
3263 GLY   ( 109-)  A 2  1.91   28
2584 GLY   (  94-)  A 1  1.88   12
3248 GLY   (  94-)  A 2  1.81   20
 758 GLY   (  94-)  A   1.80   17
 909 GLY   (  79-)  A   1.76   27
1422 GLY   (  94-)  A   1.75   16
 237 GLY   (  71-)  A   1.68   10
2267 GLY   ( 109-)  A 1  1.66   21
3228 GLY   (  74-)  A 2  1.63   21
1231 GLY   (  69-)  A   1.62   12
2231 GLY   (  73-)  A 1  1.61   18
3250 GLY   (  96-)  A 2  1.59   40
2393 GLY   (  69-)  A 1  1.58   12
1402 GLY   (  74-)  A   1.57   10
2569 GLY   (  79-)  A 1  1.55   21
1432 GLY   ( 104-)  A   1.54   17
2586 GLY   (  96-)  A 1  1.51   80
 109 GLY   ( 109-)  A   1.50   17

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

   5 PRO   (   5-)  A  -139.9 envelop C-delta (-144 degrees)
  12 PRO   (  12-)  A   -62.0 half-chair C-beta/C-alpha (-54 degrees)
  33 PRO   (  33-)  A   108.8 envelop C-beta (108 degrees)
 199 PRO   (  33-)  A   104.6 envelop C-beta (108 degrees)
 365 PRO   (  33-)  A   109.8 envelop C-beta (108 degrees)
 510 PRO   (  12-)  A    52.8 half-chair C-delta/C-gamma (54 degrees)
 531 PRO   (  33-)  A   106.5 envelop C-beta (108 degrees)
 697 PRO   (  33-)  A   107.0 envelop C-beta (108 degrees)
 863 PRO   (  33-)  A   107.3 envelop C-beta (108 degrees)
1029 PRO   (  33-)  A   103.1 envelop C-beta (108 degrees)
1160 PRO   ( 164-)  A    37.0 envelop C-delta (36 degrees)
1195 PRO   (  33-)  A   104.9 envelop C-beta (108 degrees)
1361 PRO   (  33-)  A   108.3 envelop C-beta (108 degrees)
1492 PRO   ( 164-)  A    37.9 envelop C-delta (36 degrees)
1527 PRO   (  33-)  A 1  104.2 envelop C-beta (108 degrees)
1665 PRO   (   5-)  A 1 -138.3 envelop C-delta (-144 degrees)
1672 PRO   (  12-)  A 1  -63.7 envelop C-beta (-72 degrees)
1693 PRO   (  33-)  A 1  106.4 envelop C-beta (108 degrees)
1778 PRO   ( 118-)  A 1  101.4 envelop C-beta (108 degrees)
1859 PRO   (  33-)  A 1  105.2 envelop C-beta (108 degrees)
2025 PRO   (  33-)  A 1  105.4 envelop C-beta (108 degrees)
2191 PRO   (  33-)  A 1  106.3 envelop C-beta (108 degrees)
2357 PRO   (  33-)  A 1  102.0 envelop C-beta (108 degrees)
2442 PRO   ( 118-)  A 1 -122.1 half-chair C-delta/C-gamma (-126 degrees)
2488 PRO   ( 164-)  A 1   38.2 envelop C-delta (36 degrees)
2502 PRO   (  12-)  A 1   50.1 half-chair C-delta/C-gamma (54 degrees)
2523 PRO   (  33-)  A 1  106.1 envelop C-beta (108 degrees)
2654 PRO   ( 164-)  A 1   38.1 envelop C-delta (36 degrees)
2667 PRO   (  11-)  A 1 -124.7 half-chair C-delta/C-gamma (-126 degrees)
2689 PRO   (  33-)  A 1  112.8 envelop C-beta (108 degrees)
2855 PRO   (  33-)  A 1  102.7 envelop C-beta (108 degrees)
3021 PRO   (  33-)  A 1  106.3 envelop C-beta (108 degrees)
3187 PRO   (  33-)  A 2  108.2 envelop C-beta (108 degrees)
3221 PRO   (  67-)  A 2   13.5 half-chair N/C-delta (18 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short distance.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively).

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. In any case, each bump is listed in only one direction. However, as this seems to be an NMR structure, this is unlikely to happen in this report.

1028 ALA   (  32-)  A      N   <-> 1029 PRO   (  33-)  A      CD     0.42    2.58
 530 ALA   (  32-)  A      N   <->  531 PRO   (  33-)  A      CD     0.42    2.58
2688 ALA   (  32-)  A 1    N   <-> 2689 PRO   (  33-)  A 1    CD     0.42    2.58
1692 ALA   (  32-)  A 1    N   <-> 1693 PRO   (  33-)  A 1    CD     0.42    2.58
3186 ALA   (  32-)  A 2    N   <-> 3187 PRO   (  33-)  A 2    CD     0.42    2.58
  32 ALA   (  32-)  A      N   <->   33 PRO   (  33-)  A      CD     0.42    2.58
1194 ALA   (  32-)  A      N   <-> 1195 PRO   (  33-)  A      CD     0.42    2.58
2190 ALA   (  32-)  A 1    N   <-> 2191 PRO   (  33-)  A 1    CD     0.42    2.58
 364 ALA   (  32-)  A      N   <->  365 PRO   (  33-)  A      CD     0.42    2.58
2854 ALA   (  32-)  A 1    N   <-> 2855 PRO   (  33-)  A 1    CD     0.42    2.58
2356 ALA   (  32-)  A 1    N   <-> 2357 PRO   (  33-)  A 1    CD     0.41    2.59
3020 ALA   (  32-)  A 1    N   <-> 3021 PRO   (  33-)  A 1    CD     0.41    2.59
1858 ALA   (  32-)  A 1    N   <-> 1859 PRO   (  33-)  A 1    CD     0.41    2.59
 696 ALA   (  32-)  A      N   <->  697 PRO   (  33-)  A      CD     0.41    2.59
2024 ALA   (  32-)  A 1    N   <-> 2025 PRO   (  33-)  A 1    CD     0.41    2.59
 198 ALA   (  32-)  A      N   <->  199 PRO   (  33-)  A      CD     0.41    2.59
 862 ALA   (  32-)  A      N   <->  863 PRO   (  33-)  A      CD     0.41    2.59
2522 ALA   (  32-)  A 1    N   <-> 2523 PRO   (  33-)  A 1    CD     0.41    2.59
1526 ALA   (  32-)  A 1    N   <-> 1527 PRO   (  33-)  A 1    CD     0.41    2.59
1360 ALA   (  32-)  A      N   <-> 1361 PRO   (  33-)  A      CD     0.41    2.59
3049 MET   (  61-)  A 1    SD  <-> 3101 PHE   ( 113-)  A 1    CD2    0.25    3.15
1695 THR   (  35-)  A 1    CG2 <-> 1760 MET   ( 100-)  A 1    SD     0.23    3.17
1525 HIS   (  31-)  A 1    C   <-> 1527 PRO   (  33-)  A 1    CD     0.22    2.98
2521 HIS   (  31-)  A 1    C   <-> 2523 PRO   (  33-)  A 1    CD     0.22    2.98
 197 HIS   (  31-)  A      C   <->  199 PRO   (  33-)  A      CD     0.22    2.98
And so on for a total of 445 lines.

Packing, accessibility and threading

Note: Per-model averages for inside/outside residue distributi ...heck




















Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 10

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 11

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 12

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 13

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 14

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 15

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 16

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 17

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 18

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 19

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 20

Warning: Abnormal packing environment for some residues


Warning: Abnormal packing environment for sequential residues


Error: Abnormal average packing environment

Note: Quality value plot

Chain identifier: A; Model number 1

Note: Quality value plot

Chain identifier: A; Model number 2

Note: Quality value plot

Chain identifier: A; Model number 3

Note: Quality value plot

Chain identifier: A; Model number 4

Note: Quality value plot

Chain identifier: A; Model number 5

Note: Quality value plot

Chain identifier: A; Model number 6

Note: Quality value plot

Chain identifier: A; Model number 7

Note: Quality value plot

Chain identifier: A; Model number 8

Note: Quality value plot

Chain identifier: A; Model number 9

Note: Quality value plot

Chain identifier: A; Model number 10

Note: Quality value plot

Chain identifier: A; Model number 11

Note: Quality value plot

Chain identifier: A; Model number 12

Note: Quality value plot

Chain identifier: A; Model number 13

Note: Quality value plot

Chain identifier: A; Model number 14

Note: Quality value plot

Chain identifier: A; Model number 15

Note: Quality value plot

Chain identifier: A; Model number 16

Note: Quality value plot

Chain identifier: A; Model number 17

Note: Quality value plot

Chain identifier: A; Model number 18

Note: Quality value plot

Chain identifier: A; Model number 19

Note: Quality value plot

Chain identifier: A; Model number 20

Warning: Low packing Z-score for some residues


Note: Per-model averages for NQA




















Note: Second generation quality Z-score plot

Chain identifier: A; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 2

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 3

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 4

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 5

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 6

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 7

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 8

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 9

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 10

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 11

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 12

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 13

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 14

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 15

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 16

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 17

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 18

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 19

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 20

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips


Warning: Buried unsatisfied hydrogen bond donors


Warning: Buried unsatisfied hydrogen bond acceptors


Warning: No crystallisation information

Warning: Possible wrong residue type


Final summary

Note: Summary report for users of a structure